Managed to get a file uploaded to the FT-8800, with complete success -- except for one little thing: how do I get the RIGHT side of the radio uploaded? (For those who don't have the 8800, the left and right side of the radio have completely separate memories; you can't even copy between them in the radio.)

They're all uploaded and downloaded at the same time, in a single memory image. When you open (or download) an image, you'll see two tabs along the top (in 0.3.1, or along the left side on a recent version) for the two bands. Make changes to either/both and then an upload will include both sets.